Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques/Experiment 6
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca mulatta
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Axilla skin Axillary skin,Skin of axilla,Axilla skin,axilla skin
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Microbiome measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Complete microbiome social group R
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group F
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "sampling period" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling period
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group F
| NCBI | Quality Control | Links |
|---|---|---|
| Cyanobacteriota |
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: decreased abundance in Complete microbiome social group F
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Pseudomonadota |
Revision editor(s): Fiddyhamma
